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ATE444532T1 - METHOD FOR IDENTIFYING POLYMORPHOIC GENETIC MARKERS - Google Patents

METHOD FOR IDENTIFYING POLYMORPHOIC GENETIC MARKERS

Info

Publication number
ATE444532T1
ATE444532T1 AT00972148T AT00972148T ATE444532T1 AT E444532 T1 ATE444532 T1 AT E444532T1 AT 00972148 T AT00972148 T AT 00972148T AT 00972148 T AT00972148 T AT 00972148T AT E444532 T1 ATE444532 T1 AT E444532T1
Authority
AT
Austria
Prior art keywords
nucleic acid
obtaining
mass spectrum
detecting
identifying
Prior art date
Application number
AT00972148T
Other languages
German (de)
Inventor
Andreas Braun
Hubert Koester
Den Boom Dirk Van
Yip Ping
Charlie Rodi
Liyan He
Norman Chiu
Christian Jurinke
Original Assignee
Sequenom Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US09/663,968 external-priority patent/US7917301B1/en
Application filed by Sequenom Inc filed Critical Sequenom Inc
Application granted granted Critical
Publication of ATE444532T1 publication Critical patent/ATE444532T1/en

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/40—Population genetics; Linkage disequilibrium
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/50—Compression of genetic data
    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/0027—Methods for using particle spectrometers
    • H01J49/0036—Step by step routines describing the handling of the data generated during a measurement
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Chemical & Material Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • Ecology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)

Abstract

A method for detecting methyated nucleotides within a nucleic acid sample includes the steps of treating nucleic acid molecules with bisulfite, amplifying the nucleic acid in the presence of dUTP, cleaving the amplified nucleic acid at uracil to produce fragments thereof, obtaining a mass spectrum of the resulting fragments, obtaining a mass spectrum of fragmented amplified untreated nucleic acid molecules; and detecting methylated nucleotides by identifying a difference in signals between the mass spectra. A method for detecting the presence, absence or frequency of a polymorphism in a population includes the steps of pooling each isolated biopolymers from a plurality of organisms, optionally introducing a cleavage site into the biopolymer, optionally amplifying the amount of biopolymer, cleaving the pooled biopolymers to produce fragments thereof, obtaining a mass spectrum of the resulting fragments; and determining the presence, absence or frequency of a fragment containing the polymorphism.
AT00972148T 1999-10-13 2000-10-13 METHOD FOR IDENTIFYING POLYMORPHOIC GENETIC MARKERS ATE444532T1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US15917699P 1999-10-13 1999-10-13
US21725100P 2000-07-10 2000-07-10
US21765800P 2000-07-10 2000-07-10
US09/663,968 US7917301B1 (en) 2000-09-19 2000-09-19 Method and device for identifying a biological sample
PCT/US2000/028413 WO2001027857A2 (en) 1999-10-13 2000-10-13 Methods for generating databases and databases for identifying polymorphic genetic markers

Publications (1)

Publication Number Publication Date
ATE444532T1 true ATE444532T1 (en) 2009-10-15

Family

ID=27496366

Family Applications (1)

Application Number Title Priority Date Filing Date
AT00972148T ATE444532T1 (en) 1999-10-13 2000-10-13 METHOD FOR IDENTIFYING POLYMORPHOIC GENETIC MARKERS

Country Status (9)

Country Link
EP (2) EP1261932B1 (en)
JP (2) JP2003519829A (en)
KR (1) KR20020064298A (en)
AT (1) ATE444532T1 (en)
AU (1) AU776811C (en)
CA (1) CA2387035A1 (en)
DE (1) DE60043076D1 (en)
IL (1) IL148930A0 (en)
WO (1) WO2001027857A2 (en)

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Also Published As

Publication number Publication date
EP2088209B1 (en) 2017-05-31
EP2088209A1 (en) 2009-08-12
AU776811C (en) 2005-07-28
KR20020064298A (en) 2002-08-07
EP1261932A2 (en) 2002-12-04
IL148930A0 (en) 2002-09-12
AU776811B2 (en) 2004-09-23
DE60043076D1 (en) 2009-11-12
EP1261932B1 (en) 2009-09-30
WO2001027857A3 (en) 2002-10-03
WO2001027857A2 (en) 2001-04-19
AU1084801A (en) 2001-04-23
JP2004158005A (en) 2004-06-03
JP2003519829A (en) 2003-06-24
CA2387035A1 (en) 2001-04-19
WO2001027857A9 (en) 2002-12-05

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